Sep 5 – 10, 2022
Hotel Olšanka, Prague
Europe/Prague timezone

#FijiHackathon – Collaborative development for Fiji and Friends

Fiji (Fiji Is Just ImageJ) is a popular software platform for image processing, and its community has developed and made available numerous plugins for scientific audiences.

The focus of this hackathon is on data parallelism, which requires an appropriate image format. We are believers in the NGFF to give us this functionality. During the hackathon we hope that we would marry Fiji with NGFF such that regular Fiji users could read and write any portion of their large data from Fiji macro, Jython script of using Java or Python API.

The main topics for the events are

  • Be able to read & write chunks (e.g., one full time point) from local & remote .ome.zarr from ImageJ macro (.ijm) and Jython scripts, imglib2 under the hood ...
  • GUI in Fiji (tree view + select chunks) on the local & remote .ome.zarr
  • Manuals + tutorials for users non-programmers
  • BDV support for opening .ome.zarr
  • DataStore (an alternative REST HTTP API for bi-directional, chunk-based & pyramids, remote image data access) stores .ome.zarr
  • Image data storage and generic data storage

Anyone who could tag their skills :slight_smile: with some of the following tags: Java, Python, Fiji, imglib2, zarr, ngff, BDV, wiki, tutorials and who is willing to spent time, learn, code and give a helping hand is welcomed.

If your find yourself interested :point_right: check out our Zulip channel 6 and register there please.

The event is understood as primarily on-site one. However, virtual presence is possible (…for long-distance travelers, or super-busy VIPs :slight_smile:).

This event is supported by the ERDF in the IT4Innovations national supercomputing center - path to exascale project (CZ.02.1.01/0.0/0.0/16_013/0001791) within the OPRDE.

Hotel Olšanka, Prague
Táboritská 23/1000 Praha 3
Go to map

Further details on available HPC clusters:

Registration for this event is currently open.